Transcripts Per Million

Normalize transcript length-adjusted abundances to one million TPM.

Description

TPM first corrects transcript abundance for effective length and then scales the supplied transcript set to one million.

TPM first corrects transcript abundance for effective length and then scales the supplied transcript set to one million. The normalization denominator is the sum of length-adjusted abundances.^[1]

Normalize transcript length-adjusted abundances to one million TPM.

When to use Transcripts Per Million

Use this tool to normalize transcript length-adjusted abundances to one million TPM.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use Transcripts Per Million and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter transcriptCounts, effectiveLengthsBp using the field table and calculation rules, then run the tool.
Read tpm, totalTpm. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
transcriptCounts	Transcript counts	list of number	Required
effectiveLengthsBp	Effective lengths bp	list of number	Required

Enter aligned nonempty nonnegative counts and positive effective lengths in bp, with at least one positive count. Compute rates, divide by their sum and return per-transcript TPM plus total TPM, subject to floating-point roundoff.

rate_i=count_i/(lengthBp_i/1000); TPM_i=10⁶ rate_i/Σrate

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
tpm	Tpm	list of number
totalTpm	Total tpm	number

json

{
  "input": {
    "transcriptCounts": [
      100,
      100
    ],
    "effectiveLengthsBp": [
      1000,
      2000
    ]
  },
  "output": {
    "tpm": [
      666666.6666666666,
      333333.3333333333
    ],
    "totalTpm": 1000000
  }
}

Limitations and assumptions

The result is relative to the supplied set. It does not estimate transcript assignments, effective lengths, uncertainty or cross-sample differential expression.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Fragments Per Kilobase Million: Calculate fragments per kilobase of transcript per million mapped fragments. For a complementary task, use Isoform TPM Share: Normalize isoform TPMs to within-gene usage percentages.

References

Transcripts Per Million — tool.io

Similar or alternative tools

Fragments Per Kilobase Million
Calculate fragments per kilobase of transcript per million mapped fragments.
Isoform TPM Share
Normalize isoform TPMs to within-gene usage percentages.